CaltechAUTHORS
  A Caltech Library Service
Login

Quantifying orthogonal barcodes for sequence census assays

Booeshaghi, A. Sina and Min, Kyung Hoi (Joseph) and Gehring, Jase and Pachter, Lior (2022) Quantifying orthogonal barcodes for sequence census assays. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20230322-101653000.21

[img] PDF - Submitted Version
Creative Commons Attribution.
1MB
[img] PDF - Supplemental Material
Creative Commons Attribution.
3MB

Use this Persistent URL to link to this item: https://resolver.caltech.edu/CaltechAUTHORS:20230322-101653000.21

Abstract

Barcode-based sequence census assays utilize custom or random oligonucloetide sequences to label various biological features, such as cell-surface proteins or CRISPR perturbations. These assays all rely on barcode quantification, a task that is complicated by barcode design and technical noise. We introduce a modular approach to quantifying barcodes that achieves speed and memory improvements over existing tools. We also introduce a set of quality control metrics, and accompanying tool, for validating barcode designs.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/2022.10.09.511501DOIDiscussion Paper
https://github.com/pachterlab/BMGP_2020Related Itempachterlab / BMGP_2020
https://github.com/pachterlab/kb_python/Related Itempachterlab / kb_python
https://github.com/pachterlab/qcbc/Related Itempachterlab / qcbc
ORCID:
AuthorORCID
Booeshaghi, A. Sina0000-0002-6442-4502
Min, Kyung Hoi (Joseph)0000-0003-0894-4017
Gehring, Jase0000-0002-3894-9495
Pachter, Lior0000-0002-9164-6231
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. The authors have declared no competing interest.
DOI:10.1101/2022.10.09.511501
Record Number:CaltechAUTHORS:20230322-101653000.21
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20230322-101653000.21
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:120314
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:22 Mar 2023 18:07
Last Modified:22 Mar 2023 18:07

Repository Staff Only: item control page

CaltechAUTHORS is powered by EPrints 3.3 which is developed by the School of Electronics and Computer Science at the University of Southampton. More information and software credits.